I was accepted to the CPRIT-CURE Summer Undergraduate Program at MD Anderson in Houston. There, I conducted research in the Bioinformatics & Computational Biology Department with Anil Korkut, PhD. My Project was to implement a mathematical method to analyze specific targeted therapies in order to identify their adaptive resistance behaviors in BRAF inhibitor-resistant melanoma cells.
The goal of my project was to better understand the mechanisms of the adaptive resistance as well as discovering combination therapies to overcome the resistance. I used computational methods, pathway analysis, and biostatistics to address this problem. Once the adaptation mechanisms were identified using the model, combination therapies were nominated with the intention of overcoming the resistance. I was successfully able to implement this method and was able to identify adaptive responses in BRRAF resistant melanoma cells. This technique could be used for patients with resistant melanoma to prescribe a unique therapy to fight their disease, similar to personalized medicine. I presented my work through a poster presentation.
The summer of 2016, I conducted research in the Bioinformatics and Genomics Program at LSU Health Science Center School of Medicine in New Orleans. I was able to join through the Undergraduate Student Summer Research Program. I worked with Chindo Hicks, PhD and director of the Bioinformatics and Genomics Program. My project used gene expression data to determine specific genes that can predispose women to triple negative breast cancer.
My findings have been curated into a manuscript titled, "An Integrative Genomics Approach for Associating Genetic Susceptibility with the Tumor Immune Microenvironment in Triple Negative Breast Cancer"
Elnaggar, Jacob & Tsien, Fern & Yates, Clayton & Davis, Melisa & Miele, Lucio & Hicks, Chindo. (2019). An Integrative Genomics Approach for Associating Genetic Susceptibility with the Tumor Immune Microenvironment in Triple Negative Breast Cancer. 10.26717/BJSTR.2019.15.002642.
After my acceptance to LSU School of Medicine in New Orleans, I began conducting research with Christopher Taylor, PhD. Dr. Taylor has a Bioinformatics lab in the department of Microbiology, Immunology, and Parasitology.
In his lab I began worked on analyzing the vaginal microbiota in women with chlamydia for specific microbial communities.
Now I am working Shotgun Metagenomic sequencing data in women with bacterial vaginosis.
The summer 2015, I was accepted to the LSU Health Science Center School of Medicine's Undergraduate Student Summer Research Program in New Orleans. There I conducted physiological research under Patricia Molina, MD, PhD and Head of the Department of Physiology. I investigated the combined effects of chronic binge alcohol administration and simian immunodeficiency virus on cell apoptosis in the prefrontal cortex of Rhesus macaque monkeys. I measured this through western blots and staining. I found that the combined stimuli resulted in a significant increase in neuronal cell death, and I presented my findings through a poster presentation.
At Baylor University, I conducted research with Marty Harvill, PhD. With him, I studied the soil fertility of the Lake Waco Wetlands. These wetlands are where a majority of the city collects its drinking water. The objective of this project was to test the fertility of the soil as an indicator of the quality of the water before it is treated. My project consisted of collecting soil samples from different regions and analyzing its contents. I found that there are significantly varying soil qualities throughout the different regions of the wetlands. I presented my findings through a poster presentation and a research paper. This was my initial introduction to the field of research.